Variant report

Variant	rs3829963
Chromosome Location	chr6:36644386-36644387
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr6:36643935-36644476	GM12878	blood:	n/a	chr6:36643975-36643987 chr6:36643945-36643956
2	RFX5	chr6:36644157-36644485	HepG2	liver:	n/a	chr6:36644203-36644212
3	MTA3	chr6:36643664-36644402	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:36643857-36644554	HepG2	liver:	n/a	n/a
5	NR3C1	chr6:36643988-36644406	A549	lung:	n/a	n/a
6	RAD21	chr6:36643874-36649108	SK-N-SH	brain:	n/a	chr6:36644187-36644201 chr6:36646425-36646439 chr6:36646938-36646951 chr6:36647756-36647766 chr6:36644031-36644045
7	POLR2A	chr6:36644059-36644404	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:36643863-36644528	GM12878	blood:	n/a	n/a
9	RUNX3	chr6:36643732-36644486	GM12878	blood:	n/a	n/a
10	WRNIP1	chr6:36644256-36644525	GM12878	blood:	n/a	n/a
11	MXI1	chr6:36643959-36649033	IMR90	lung:	n/a	n/a
12	MBD4	chr6:36643950-36644562	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:36643939-36647410	HepG2	liver:	n/a	n/a
14	MAX	chr6:36644028-36644471	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:36643865-36644605	GM12891	blood:	n/a	n/a
16	NFIC	chr6:36644012-36644541	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:36643925-36644579	HepG2	liver:	n/a	n/a
18	EP300	chr6:36643831-36644467	GM12878	blood:	n/a	n/a
19	STAT1	chr6:36643703-36644527	Hela-S3	cervix:	n/a	chr6:36643975-36643987 chr6:36643945-36643956
20	MAX	chr6:36643823-36648608	HepG2	liver:	n/a	chr6:36648002-36648011
21	POLR2A	chr6:36644235-36644535	HCT-116	colon:	n/a	n/a
22	POLR2A	chr6:36643723-36644608	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:36643943-36644545	H1-hESC	embryonic stem cell:	n/a	n/a
24	FOS	chr6:36644155-36644421	MCF10A-Er-Src	breast:	n/a	chr6:36644202-36644211
25	CEBPB	chr6:36644078-36644542	HepG2	liver:	n/a	chr6:36644204-36644212
26	MXI1	chr6:36643752-36648956	SK-N-SH	brain:	n/a	n/a
27	TAF1	chr6:36643920-36644516	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:36643713-36644535	GM12892	blood:	n/a	n/a
29	TBP	chr6:36643838-36644642	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:36644081-36649028	IMR90	lung:	n/a	n/a
31	MYBL2	chr6:36643703-36644625	HepG2	liver:	n/a	n/a
32	EBF1	chr6:36643757-36644394	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:36643734-36644585	GM12878	blood:	n/a	n/a
34	RELA	chr6:36643834-36644495	GM19193	blood:	n/a	chr6:36644047-36644056 chr6:36644047-36644056
35	POLR2A	chr6:36643728-36644668	GM12891	blood:	n/a	n/a
36	YY1	chr6:36643940-36644440	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:36643794-36644573	GM12878	blood:	n/a	n/a
38	MTA3	chr6:36643779-36644593	GM12878	blood:	n/a	n/a
39	MYC	chr6:36644145-36644498	MCF10A-Er-Src	breast:	n/a	n/a
40	CHD1	chr6:36644011-36644540	GM12878	blood:	n/a	n/a
41	SPI1	chr6:36643636-36644409	GM12878	blood:	n/a	chr6:36644026-36644039 chr6:36643975-36643988 chr6:36643977-36643984 chr6:36643974-36643987
42	TAF1	chr6:36644075-36644404	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr6:36644149-36644553	HepG2	liver:	n/a	n/a
44	MYBL2	chr6:36643933-36646660	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:36644025-36644523	HepG2	liver:	n/a	n/a
46	STAT3	chr6:36644327-36644600	MCF10A-Er-Src	breast:	n/a	n/a
47	HEY1	chr6:36643701-36644611	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:36643627-36647609	HepG2	liver:	n/a	n/a
49	TAF1	chr6:36643999-36644479	H1-hESC	embryonic stem cell:	n/a	n/a
50	STAT5A	chr6:36643773-36644637	GM12878	blood:	n/a	chr6:36643975-36643987

No.	Distal block	Cell Line	Cell type
1	chr6:36562081..36564755-chr6:36642636..36644724,2	K562	blood:
2	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
3	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
4	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
5	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
CDKN1A	TF binding region
ENSG00000263894	Chromatin interaction
ENSG00000255587	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1010423	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1010424	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10456441	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10456442	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10456443	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1059234	0.85[JPT][hapmap]
rs10807170	0.80[LWK][hapmap]
rs10947616	0.82[ASN][1000 genomes]
rs10947618	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947620	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947622	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758192	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12174270	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192827	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192877	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12203953	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12206430	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12210094	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12214686	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12524435	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12528248	0.90[JPT][hapmap]
rs12528913	0.83[ASN][1000 genomes]
rs12530170	1.00[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1801270	0.90[JPT][hapmap]
rs3829965	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4464789	0.87[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4711458	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711459	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711460	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711461	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711462	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713993	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4714002	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714003	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58714705	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457932	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6457934	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457935	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6920453	0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6931097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72853320	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7382183	0.83[ASN][1000 genomes]
rs7747146	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7757749	0.90[JPT][hapmap]
rs7761648	0.90[JPT][hapmap]
rs876581	0.90[JPT][hapmap]
rs9349002	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9349003	0.82[ASN][1000 genomes]
rs9349005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357222	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366912	0.87[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9394371	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3829963	MLN	cis	cerebellum	SCAN
rs3829963	MAPK13	cis	parietal	SCAN
rs3829963	CDKN1A	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
2	chr6:36640400-36645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:36642400-36646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36643400-36644800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:36643600-36644600	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr6:36643600-36644800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:36643600-36646000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:36643800-36644400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:36643800-36644400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:36643800-36644400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:36643800-36644400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:36643800-36644600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:36643800-36644600	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:36643800-36644600	Flanking Active TSS	HSMMtube	muscle
15	chr6:36643800-36645000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:36643800-36645400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:36643800-36645400	Enhancers	NHDF-Ad	bronchial
18	chr6:36643800-36645600	Enhancers	Adipose Nuclei	Adipose
19	chr6:36643800-36645600	Enhancers	Brain Angular Gyrus	brain
20	chr6:36643800-36645600	Enhancers	Fetal Intestine Large	intestine
21	chr6:36643800-36645600	Enhancers	Fetal Intestine Small	intestine
22	chr6:36643800-36645600	Enhancers	A549	lung
23	chr6:36643800-36645600	Enhancers	NHLF	lung
24	chr6:36643800-36645600	Enhancers	Osteobl	bone
25	chr6:36643800-36645800	Enhancers	HUVEC	blood vessel
26	chr6:36643800-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:36643800-36646000	Enhancers	Brain Substantia Nigra	brain
28	chr6:36643800-36646000	Enhancers	NH-A	brain
29	chr6:36643800-36646200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:36643800-36646200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:36643800-36646400	Bivalent Enhancer	Fetal Thymus	thymus
32	chr6:36643800-36646400	Enhancers	Pancreas	Pancrea
33	chr6:36643800-36646400	Enhancers	Stomach Mucosa	stomach
34	chr6:36643800-36646400	Flanking Active TSS	NHEK	skin
35	chr6:36644000-36644400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr6:36644000-36644400	Enhancers	Spleen	Spleen
37	chr6:36644000-36644600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:36644000-36644600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:36644000-36644600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:36644000-36644600	Enhancers	Fetal Heart	heart
41	chr6:36644000-36644800	Active TSS	Brain Hippocampus Middle	brain
42	chr6:36644000-36644800	Active TSS	Stomach Smooth Muscle	stomach
43	chr6:36644000-36645000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:36644000-36645400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr6:36644000-36645400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr6:36644000-36645400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr6:36644000-36645600	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:36644000-36645600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr6:36644000-36645600	Enhancers	Hela-S3	cervix
50	chr6:36644000-36646000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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